Development Delay Track Settings
 
Copy Number Variation Morbidity Map of Developmental Delay   (All Phenotype and Literature tracks)

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 Case  Copy Number Variation Morbidity Map of Developmental Delay - Case   Schema 
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Description

Enrichment of large copy number variants (CNVs) has been linked to severe pediatric disease including developmental delay, intellectual disability and autism spectrum disorder. The association of individual loci with specific disorders, however, has still been problematic.

This track shows CNVs from cases of developmental delay along with healthy control sets from two separate studies. The study by Cooper et al. (2011) analyzed samples from 15,767 children with various developmental disabilities and compared them with samples from 8,329 adult controls to produce a detailed genome-wide morbidity map of developmental delay and congenital birth defects. The study by Coe et al. (2014) further expanded the morbidity map by analyzing 13,318 new case samples along with 11,255 new controls.

Display Conventions and Configuration

This is a composite track consisting of a Case subtrack and a Control subtrack. To turn a subtrack on or off, toggle the checkbox to the left of the subtrack name in the track controls at the top of the track description page.

Items in this track are colored red for copy number loss and blue for copy number gain.

Methods

The samples were analyzed using nine different CGH platforms with initial CNV calls filtered as described in Coe et al. (2014).

Final CNV calls were decoupled from identifying information and submitted to dbVar as nstd54 and nstd100 for unrestricted release.

The 15,767 case individuals from the Cooper study comprise nstd54 sampleset 1, while the 8,329 control individuals from the Cooper study comprise nstd54 samplesets 2-12. The 13,318 case individuals from the Coe study were combined with the Cooper case individuals to comprise nstd100 sampleset 1. The 11,255 control individuals from the Coe study comprise nsdt100 samplesets 2 and 3.

The Case subtrack was constructed using nstd100 sampleset 1. The Control subtrack was constructed by combining nstd100 samplesets 2 and 3 with nstd54 samplesets 2-12.

Credits

We would like to thank Gregory Cooper, Brad Coe and the Eichler Lab at the University of Washington for providing the data for this track.

References

Coe BP, Witherspoon K, Rosenfeld JA, van Bon BW, Vulto-van Silfhout AT, Bosco P, Friend KL, Baker C, Buono S, Vissers LE et al. Refining analyses of copy number variation identifies specific genes associated with developmental delay. Nat Genet. 2014 Oct;46(10):1063-71. PMID: 25217958; PMC: PMC4177294

Cooper GM, Coe BP, Girirajan S, Rosenfeld JA, Vu TH, Baker C, Williams C, Stalker H, Hamid R, Hannig V et al. A copy number variation morbidity map of developmental delay. Nat Genet. 2011 Aug 14;43(9):838-46. PMID: 21841781; PMC: PMC3171215